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Deng C, Xiong C, Huo J, Liu Y, Man Y, Qu Y. Posterior open wound healing in immediate implant placement using reactive soft tissue versus absorbable collagen sponge: a retrospective cohort study. Int J Oral Maxillofac Surg 2024; 53:436-443. [PMID: 38103945 DOI: 10.1016/j.ijom.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 10/13/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
The soft and hard tissue healing of open wounds in immediate implant placement are yet to be explored. The aim of this study was to compare the clinical outcomes of open wound healing using reactive soft tissue (RST) and absorbable collagen sponge (ACS). Forty implants placed immediately in posterior sockets were included; autologous RST was used in 20 and ACS substitute was used in 20. Soft tissue healing was primarily assessed through a novel scoring system and the evaluation of gingival recession. The horizontal bone width (HBW) and interproximal marginal bone level (MBL) were measured on radiographs to observe the hard tissue healing. No significant difference in total soft tissue healing score was observed at 2 weeks postoperatively. Notably, the ACS group showed better tissue colour (P = 0.016) but worse fibrous repair (P = 0.043) scores than the RST group. Gingival recession levels were comparable in the two groups, both before tooth extraction and after placement of the restoration. Regarding hard tissue, HBW and MBL changes showed no intergroup differences. Within the limitations of this study, both RST and ACS seemed effective for open wound closure, achieving ideal soft and hard tissue healing in immediate implant placement.
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Affiliation(s)
- C Deng
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - C Xiong
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - J Huo
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Y Liu
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Y Man
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Y Qu
- State Key Laboratory of Oral Diseases and National Center for Stomatology and National Clinical Research Center for Oral Diseases and Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.
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Deng C, Xie Y, Liu F, Tang X, Fan L, Yang X, Chen Y, Zhou Z, Li X. Simplified integration of optimal self-management behaviors is associated with improved HbA1c in patients with type 1 diabetes. J Endocrinol Invest 2024:10.1007/s40618-024-02357-8. [PMID: 38602658 DOI: 10.1007/s40618-024-02357-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE Living with type 1 diabetes requires burdensome and complex daily diabetes self-management behaviors. This study aimed to determine the association between integrated behavior performance and HbA1c, while identifying the behavior with the most significant impact on HbA1c. METHODS A simple and feasible questionnaire was used to collect diabetes self-management behavior in patients with type 1 diabetes (n = 904). We assessed six dimensions of behavior performance: continuous glucose monitor (CGM) usage, frequent glucose testing, insulin pump usage, carbohydrate counting application, adjustment of insulin doses, and usage of apps for diabetes management. We evaluated the association between these behaviors and HbA1c. RESULTS In total, 21.3% of patients performed none of the allotted behavior, while 28.5% of patients had a total behavior score of 3 or more. 63.6% of patients with a behavior score ≥ 3 achieved HbA1c goal, contrasting with only 30.4% of patients with a behavior score of 0-1. There was a mean 0.54% ± 0.05% decrease in HbA1c for each 1-unit increase in total behavior score after adjustment for age, family education and diabetes duration. Each behavior was independently correlated with a lower HbA1c level, with CGM having the most significant effect on HbA1c levels. CONCLUSIONS Six optimal self-management behaviors, especially CGM usage, were associated with improved glycemic control, emphasizing the feasibility of implementing a simplified version of DSMES in the routine clinical care. REGISTRATION NUMBER ClinicalTrials.gov Identifier: NCT03610984.
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Affiliation(s)
- C Deng
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Y Xie
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China
| | - F Liu
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China
| | - X Tang
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China
| | - L Fan
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China
| | - X Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Y Chen
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Z Zhou
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China.
| | - X Li
- Department of Metabolism and Endocrinology, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital of Central South University, Changsha, China.
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Li J, Zheng G, Jiang D, Deng C, Zhang Y, Ma Y, Su J. Mendelian randomization analysis reveals a causal effect of Streptococcus salivarius on diabetic retinopathy through regulating host fasting glucose. J Cell Mol Med 2024; 28:e18200. [PMID: 38506069 PMCID: PMC10951888 DOI: 10.1111/jcmm.18200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Diabetic retinopathy (DR) is one of leading causes of vision loss in adults with increasing prevalence worldwide. Increasing evidence has emphasized the importance of gut microbiome in the aetiology and development of DR. However, the causal relationship between gut microbes and DR remains largely unknown. To investigate the causal associations of DR with gut microbes and DR risk factors, we employed two-sample Mendelian Randomization (MR) analyses to estimate the causal effects of 207 gut microbes on DR outcomes. Inputs for MR included Genome-wide Association Study (GWAS) summary statistics of 207 taxa of gut microbes (the Dutch Microbiome Project) and 21 risk factors for DR. The GWAS summary statistics data of DR was from the FinnGen Research Project. Data analysis was performed in May 2023. We identified eight bacterial taxa that exhibited significant causal associations with DR (FDR < 0.05). Among them, genus Collinsella and species Collinsella aerofaciens were associated with increased risk of DR, while the species Bacteroides faecis, Burkholderiales bacterium_1_1_47, Ruminococcus torques, Streptococcus salivarius, genus Burkholderiales_noname and family Burkholderiales_noname showed protective effects against DR. Notably, we found that the causal effect of species Streptococcus salivarius on DR was mediated through the level of host fasting glucose, a well-established risk factor for DR. Our results reveal that specific gut microbes may be causally linked to DR via mediating host metabolic risk factors, highlighting potential novel therapeutic or preventive targets for DR.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Gongwei Zheng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Dingping Jiang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Chunyu Deng
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Yaru Zhang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Yunlong Ma
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
| | - Jianzhong Su
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye HospitalWenzhou Medical UniversityWenzhouChina
- Department of Biomedical Informatics, Institute of Biomedical Big DataWenzhou Medical UniversityWenzhouChina
- Oujiang LaboratoryZhejiang Lab for Regenerative Medicine, Vision and Brain HealthWenzhouChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouChina
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Ma Y, Zhou Y, Jiang D, Dai W, Li J, Deng C, Chen C, Zheng G, Zhang Y, Qiu F, Sun H, Xing S, Han H, Qu J, Wu N, Yao Y, Su J. Integration of human organoids single-cell transcriptomic profiles and human genetics repurposes critical cell type-specific drug targets for severe COVID-19. Cell Prolif 2024; 57:e13558. [PMID: 37807299 PMCID: PMC10905359 DOI: 10.1111/cpr.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023] Open
Abstract
Human organoids recapitulate the cell type diversity and function of their primary organs holding tremendous potentials for basic and translational research. Advances in single-cell RNA sequencing (scRNA-seq) technology and genome-wide association study (GWAS) have accelerated the biological and therapeutic interpretation of trait-relevant cell types or states. Here, we constructed a computational framework to integrate atlas-level organoid scRNA-seq data, GWAS summary statistics, expression quantitative trait loci, and gene-drug interaction data for distinguishing critical cell populations and drug targets relevant to coronavirus disease 2019 (COVID-19) severity. We found that 39 cell types across eight kinds of organoids were significantly associated with COVID-19 outcomes. Notably, subset of lung mesenchymal stem cells increased proximity with fibroblasts predisposed to repair COVID-19-damaged lung tissue. Brain endothelial cell subset exhibited significant associations with severe COVID-19, and this cell subset showed a notable increase in cell-to-cell interactions with other brain cell types, including microglia. We repurposed 33 druggable genes, including IFNAR2, TYK2, and VIPR2, and their interacting drugs for COVID-19 in a cell-type-specific manner. Overall, our results showcase that host genetic determinants have cellular-specific contribution to COVID-19 severity, and identification of cell type-specific drug targets may facilitate to develop effective therapeutics for treating severe COVID-19 and its complications.
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Affiliation(s)
- Yunlong Ma
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Yijun Zhou
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Dingping Jiang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jingjing Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Cheng Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Gongwei Zheng
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Yaru Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Fei Qiu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Haojun Sun
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Shilai Xing
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
| | - Haijun Han
- School of Medicine, Hangzhou City University, Hangzhou, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Nan Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
| | - Jianzhong Su
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Biomedical Informatics, Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Zhejiang, China
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Deng C, Zhou Y. [The life and works of Li Shouxian, a medical doctor in the Qing Dynasty]. Zhonghua Yi Shi Za Zhi 2024; 54:17-22. [PMID: 38475681 DOI: 10.3760/cma.j.cn112155-20230106-00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Li Shouxian, styled as Shanshu, was a medical doctor in the Qing Dynasty. His work Zhenjiu Yixue (Easy Study of Acupuncture and Moxibustion) has numerous versions, with the most refined one being the self-engraved edition from the third year of Jiaqing's reign, housed in the Jilin Province Library. While most content of the book was drawn from Zhenjiu Dacheng (Great Compendium of Acupuncture and Moxibustion), Li's condensation and arrangement of the material achieved the purpose of making it simple and easy to learn. The book has been widely spread and holds certain academic and historical value. This paper makes a textual research on Li's life, family, and his works, clarifies the content, structure and origin of the version of Zhenjiu Yixue and corrects errors in the version records of this book in the General Catalogue of Chinese Ancient Medical Books.
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Affiliation(s)
- C Deng
- Institute of Chinese Medical Literature and Culture, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Y Zhou
- Institute of Chinese Medical Literature and Culture, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
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Yu S, Zeng L, Rao F, Deng C, Zhang M, Xiao H, Xiao F, Xue Y, Wu S, Du Z, Wei W. High hydrostatic pressure participates in atrial fibrosis through the p300/p53/Smad3 pathway. FASEB J 2024; 38:e23324. [PMID: 38019188 DOI: 10.1096/fj.202300473rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 10/01/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023]
Abstract
As an independent risk factor of atrial fibrillation (AF), hypertension (HTN) can induce atrial fibrosis through cyclic stretch and hydrostatic pressure. The mechanism by which high hydrostatic pressure promotes atrial fibrosis is unclear yet. p300 and p53/Smad3 play important roles in the process of atrial fibrosis. This study investigated whether high hydrostatic pressure promotes atrial fibrosis by activating the p300/p53/Smad3 pathway. Biochemical experiments were used to study the expression of p300/p53/Smad3 pathway in left atrial appendage (LAA) tissues of patients with sinus rhythm (SR), AF, AF + HTN, and C57/BL6 mice, hypertensive C57/BL6 mice and atrial fibroblasts of mice. To investigate the roles of p300 and p53 in the process of atrial fibrosis, p300 and p53 in mice atrial fibroblasts were knocked in or knocked down, respectively. The expression of p300/p53/Smad3 and fibrotic factors was higher in patients with AF and AF + HTN than those with SR only. The expressions of p300/p53/Smad3 and fibrotic factors increased in hypertensive mice. Curcumin (Cur) and knocking down of p300 reversed the expressions of these factors. 40 mmHg hydrostatic pressure/overexpression of p300 upregulated the expressions of p300/p53/Smad3 and fibrotic factors in mice LAA fibroblasts. While Cur or knocking down p300 reversed these changes. Knocking down/overexpression of p53, the expressions of p53/Smad3 and fibrotic factors also decreased/increased, correspondingly. High hydrostatic pressure promotes atrial fibrosis by activating the p300/p53/Smad3 pathway, which further increases the susceptibility to AF.
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Affiliation(s)
- Shenghuan Yu
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
| | - Long Zeng
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
| | - Fang Rao
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P. R. China
| | - Chunyu Deng
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P. R. China
| | - Mengzhen Zhang
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P. R. China
| | - Haiyin Xiao
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P. R. China
| | - Feifei Xiao
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
| | - Yumei Xue
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
| | - Shulin Wu
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
| | - Zhimin Du
- Dongguan Tungwah Songshan Lake Hospital, Dongguan, P.R. China
| | - Wei Wei
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, P.R. China
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7
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Lai Y, He J, Gao X, Peng D, Zhou H, Xu Y, Luo X, Yang H, Zhang M, Deng C, Wu S, Xue Y, Zhou F, Rao F. Involvement of plasminogen activator inhibitor-1 in p300/p53-mediated age-related atrial fibrosis. PeerJ 2023; 11:e16545. [PMID: 38107584 PMCID: PMC10722982 DOI: 10.7717/peerj.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/08/2023] [Indexed: 12/19/2023] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1), a key regulator of the fibrinolytic system, is also intimately involved in the fibrosis. Although PAI-1 may be involved in the occurrence of atrial fibrillation (AF) and thrombosis in the elderly, but whether it participated in aging-related atrial fibrosis and the detailed mechanism is still unclear. We compared the transcriptomics data of young (passage 4) versus senescent (passage 14) human atrial fibroblasts and found that PAI-1 was closely related to aging-related fibrosis. Aged mice and senescent human and mouse atrial fibroblasts underwent electrophysiological and biochemical studies. We found that p300, p53, and PAI-1 protein expressions were increased in the atrial tissue of aged mice and senescent human and mouse atrial fibroblasts. Curcumin or C646 (p300 inhibitor), or p300 knockdown inhibited the expression of PAI-1 contributing to reduced atrial fibroblasts senescence, atrial fibrosis, and the AF inducibility. Furthermore, p53 knockdown decreased the protein expression of PAI-1 and p21 in senescent human and mouse atrial fibroblasts. Our results suggest that p300/p53/PAI-1 signaling pathway participates in the mechanism of atrial fibrosis induced by aging, which provides new sights into the treatment of elderly AF.
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Affiliation(s)
- Yingyu Lai
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- Department of Pharmacy, The People’s Hospital of Hezhou, Hezhou, Guangxi, China
| | - Jintao He
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiaoyan Gao
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Dewei Peng
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Huishan Zhou
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yuwen Xu
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xueshan Luo
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hui Yang
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Mengzhen Zhang
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chunyu Deng
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Shulin Wu
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yumei Xue
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Feng Zhou
- Department of Neurology, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Fang Rao
- Medical Research Institute, Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
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Wang M, Deng C, Yang C, Yan M, Lu H, Zhang Y, Liu H, Tong Z, Ma J, Wang J, Zhang Y, Wang J, Xuan Y, Cheng H, Zhao K, Zhang J, Chai C, Li M, Yu Z. Unraveling temporal and spatial biomarkers of epithelial-mesenchymal transition in colorectal cancer: insights into the crucial role of immunosuppressive cells. J Transl Med 2023; 21:794. [PMID: 37940972 PMCID: PMC10633927 DOI: 10.1186/s12967-023-04600-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
The occurrence and progression of tumors can be established through a complex interplay among tumor cells undergoing epithelial-mesenchymal transition (EMT), invasive factors and immune cells. In this study, we employed single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (ST) to evaluate the pseudotime trajectory and spatial interactive relationship between EMT-invasive malignant tumors and immune cells in primary colorectal cancer (CRC) tissues at different stages (stage I/II and stage III with tumor deposit). Our research characterized the spatiotemporal relationship among different invasive tumor programs by constructing pseudotime endpoint-EMT-invasion tumor programs (EMTPs) located at the edge of ST, utilizing evolution trajectory analysis integrated with EMT-invasion genes. Strikingly, the invasive and expansive process of tumors undergoes remarkable spatial reprogramming of regulatory and immunosuppressive cells, such as myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs), regulatory T cells (Treg), and exhausted T cells (Tex). These EMTP-adjacent cell are linked to EMT-related invasion genes, especially the C-X-C motif ligand 1 (CXCL1) and CXCL8 genes that are important for CRC prognosis. Interestingly, the EMTPs in stage I mainly produce an inflammatory margin invasive niche, while the EMTPs in stage III tissues likely produce a hypoxic pre-invasive niche. Our data demonstrate the crucial role of regulatory and immunosuppressive cells in tumor formation and progression of CRC. This study provides a framework to delineate the spatiotemporal invasive niche in CRC samples.
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Affiliation(s)
- Muhong Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Cheng Yang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Mingze Yan
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Haibo Lu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Yan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Honghao Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Zhekuan Tong
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Jiaao Ma
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Jiaming Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Yan Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Jiahao Wang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Yuhong Xuan
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Haiyue Cheng
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Kai Zhao
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Jiaqi Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Cuicui Chai
- Digestive Disease Center, The Seventh Affiliated Hospital Sun Yat-Sen University, Shenzhen, 518107, China
| | - Mingzhe Li
- Digestive Disease Center, The Seventh Affiliated Hospital Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
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Ma Y, Deng C, Zhou Y, Zhang Y, Qiu F, Jiang D, Zheng G, Li J, Shuai J, Zhang Y, Yang J, Su J. Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data. Cell Genom 2023; 3:100383. [PMID: 37719150 PMCID: PMC10504677 DOI: 10.1016/j.xgen.2023.100383] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/26/2023] [Accepted: 07/25/2023] [Indexed: 09/19/2023]
Abstract
Advances in single-cell RNA sequencing (scRNA-seq) techniques have accelerated functional interpretation of disease-associated variants discovered from genome-wide association studies (GWASs). However, identification of trait-relevant cell populations is often impeded by inherent technical noise and high sparsity in scRNA-seq data. Here, we developed scPagwas, a computational approach that uncovers trait-relevant cellular context by integrating pathway activation transformation of scRNA-seq data and GWAS summary statistics. scPagwas effectively prioritizes trait-relevant genes, which facilitates identification of trait-relevant cell types/populations with high accuracy in extensive simulated and real datasets. Cellular-level association results identified a novel subpopulation of naive CD8+ T cells related to COVID-19 severity and oligodendrocyte progenitor cell and microglia subsets with critical pathways by which genetic variants influence Alzheimer's disease. Overall, our approach provides new insights for the discovery of trait-relevant cell types and improves the mechanistic understanding of disease variants from a pathway perspective.
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Affiliation(s)
- Yunlong Ma
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150080, China
| | - Yijun Zhou
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Yaru Zhang
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Fei Qiu
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Dingping Jiang
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Gongwei Zheng
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jingjing Li
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jianwei Shuai
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
| | - Yan Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150080, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310012, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of OphthalmoFlogy & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang 325101, China
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10
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Yang ST, Deng C, He BB, Chen X, Li X, Zhou ZG. [Application of the Chinese Expert Consensus on Diabetes Classification in clinical practice]. Zhonghua Nei Ke Za Zhi 2023; 62:1085-1092. [PMID: 37650182 DOI: 10.3760/cma.j.cn112138-20230131-00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Objective: To evaluate the diagnostic for classification of newly diagnosed diabetes patients and assess the application of the screening tests recommended by the 2022 Chinese Expert Consensus on Diabetes Classification. Methods: Retrospective case series study. The data from the electronic medical record system of patients with new-onset diabetes mellitus (within 1 year of disease onset) who attending the Diabetes Specialist Outpatient Clinic at the Second Xiangya Hospital of Central South University from January 1, 2018 to December 31, 2021 were collected for the analysis. Based on the consensus, patients were categorized according their age of onset, body mass index (BMI), and suspicion of type 1 diabetes mellitus (T1DM). The chi-square statistic was used to compare key classifier indicators, including C-peptide, islet autoantibodies, and genetic markers, in the subgroups. The diagnosis in suspected T1DM patients was also evaluated. The screening strategy recommended in the consensus was further assessed using a logistic regression model and the area under the receiver-operating curve (AUC). Results: A total of 3 384 patients with new-onset diabetes were included. The average age of disease onset was (46.3±13.9) years, and 61.0% (2 065/3 384) of the patients were male. The proportions of patients who completed C-peptide and glutamic acid decarboxylase antibody (GADA) tests were 36.6% (1 238/3 384) and 37.5% (1 269/3 384), respectively. There were no significant differences in C-peptide test results among the subgroups (all P>0.05). In contrast, the GADA detection rate was higher in patients with young age of onset (<30 years old), in those who were non-obese (BMI<24 kg/m2), and in those clinically suspected of T1DM (all P<0.05). According to the diagnostic pathway proposed by the consensus, only 57.4% (1 941/3 384) of patients could be subtyped. For a definitive diagnosis, the remaining patients needed completion of C-peptide, islet autoantibody, genetic testing, or follow-up. Furthermore, among patients with clinical features of suspected T1DM, the antibody positivity rate was higher than in non-suspected T1DM patients [24.5% (154/628) vs. 7.1% (46/646), P<0.001]. When the clinical features of suspected T1DM defined in the consensus were taken as independent variables and antibody positivity was considered the outcome variable in the logistic regression model, young onset, non-obese onset, and ketosis onset could enter the model. Based on AUC analysis, the accuracy of the diagnostic model was 0.77 (95%CI 0.73-0.81), suggesting that the clinical features of suspected T1DM in the consensus have good clinical diagnostic value for this patient subgroup. Conclusions: There was a significant discrepancy between the clinical practice of diabetes classification and the process recommended by the consensus, which was specifically reflected in the low proportions of both subtyping indicator testing and definitively subtyped diabetes patients. Attention should be pay to the classification diagnosis process proposed in the consensus and the clinical detection rate of key diabetes subtyping indicators such as C-peptide and islet autoantibodies for diabetes classification should be improved. Noteworthy, the screening strategy for T1DM proposed by the consensus showed good clinical application value.
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Affiliation(s)
- S T Yang
- Department of Metabolism and Endocrinology, the Second Xiangya Hospital of Central South University, National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Changsha 410011, China
| | - C Deng
- Department of Metabolism and Endocrinology, the Second Xiangya Hospital of Central South University, National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Changsha 410011, China
| | - B B He
- Department of Metabolism and Endocrinology, the Second Xiangya Hospital of Central South University, National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Changsha 410011, China
| | - X Chen
- Department of Information Science, the Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - X Li
- Department of Metabolism and Endocrinology, the Second Xiangya Hospital of Central South University, National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Changsha 410011, China
| | - Z G Zhou
- Department of Metabolism and Endocrinology, the Second Xiangya Hospital of Central South University, National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology, Ministry of Education, Changsha 410011, China
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11
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Li B, Chen X, Hu J, Ke G, Jiang N, Zhang F, Lian Z, Wen S, Wu Q, Xia Y, Zhang H, Kuang S, Xu L, Deng C, Liu S. COMMD5 is involved in the mechanisms of hypotension after parathyroidectomy in patients receiving hemodialysis. Eur J Pharmacol 2023; 944:175596. [PMID: 36804542 DOI: 10.1016/j.ejphar.2023.175596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Secondary hyperparathyroidism (SHPT) is a common complication of end-stage renal disease. Parathyroidectomy (PTx) is often employed for treatment of severe SHPT. However, PTx may cause hypotension via unknown mechanisms. COMM domain-containing protein 5 (COMMD5) in the parathyroid glands has been linked to blood pressure regulation of spontaneously hypertensive rats. OBJECTIVE To explore the relationship between COMMD5 levels and reduced BP after PTx in patients receiving hemodialysis (HD). METHODS AND RESULTS (1) The study cohort included 31 patients receiving HD who underwent PTx. Serum COMMD5 levels were higher post-PTx vs. pre-PTx. (2) Sprague-Dawley rats (n = 22) were assigned to a 5/6 nephrectomy group or sham surgery group, vascular rings of the thoracic aorta from rats with CKD were incubated with COMMD5, and changes in vascular tension were compared. COMMD5 inhibited vasoconstriction of vascular rings with intact endothelium, but had no effect on vascular rings without the endothelium. (3) Human umbilical vein endothelial cells were stimulated with COMMD5 or small interfering RNA (siRNA). The expression levels of atrial natriuretic peptide (ANP) and endothelial nitric oxide synthase (eNOS) were up-regulated and down-regulated, respectively. CONCLUSIONS Serum COMMD5 levels were increased after PTx in SHPT patients. COMMD5 promoted high expression of ANP and eNOS in endothelial cells, leading to vasodilation and resulting in hypotension.
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Affiliation(s)
- Bohou Li
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xueqin Chen
- Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, China
| | - Juan Hu
- The Fourth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guibao Ke
- Department of Nephrology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Nan Jiang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China; School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Fengxia Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhiwen Lian
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Sichun Wen
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China; School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Qiong Wu
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yubin Xia
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hong Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China; School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Sujuan Kuang
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Medical Research Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Lixia Xu
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Chunyu Deng
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Medical Research Center, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Shuangxin Liu
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
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12
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Sun Y, Wang D, Deng C, Lu M, Zhu W, Yun B, Hu G, Cui Y. Frequency-selectable microwave generation based on on-chip switchable spectral shaping and wavelength-to-time mapping. Opt Express 2023; 31:3179-3186. [PMID: 36785315 DOI: 10.1364/oe.478146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
We propose and experimentally demonstrate a scheme for the photonic generation of pulsed microwave signals with selectable frequency based on spectral shaping and wavelength-to-time mapping (WTTM) technique. The frequency selectivity is realized by channel switching on an integrated silicon-on-insulator (SOI) spectral shaping chip. The incident signal is spectrally shaped by the asymmetric Mach-Zehnder interferometer (MZI) in the selected channel, and an optical spectrum with uniform free spectral range (FSR) can be generated in a broad bandwidth up to dozens of nanometers, implying large microwave signal duration after WTTM if a pulse light source with matched bandwidth is available. Microwave pulses of frequency from 3.6 GHz to 28.4 GHz with a fixed interval are experimentally generated respectively. The realization of eight microwave frequencies selectable with only one shared dispersive element (DE) required indicates high expansibility in the frequency cover range of our scheme by tuning the dispersion value in WTTM.
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13
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Zhang P, Ohshima S, Zhao H, Deng C, Kobayashi S, Kado S, Minami T, Matoike R, Miyashita A, Iwata A, Kondo Y, Qiu D, Wang C, Luo M, Konoshima S, Inagaki S, Okada H, Mizuuchi T, Nagasaki K. Development and initial results of 320 GHz interferometer system in Heliotron J. Rev Sci Instrum 2022; 93:113519. [PMID: 36461432 DOI: 10.1063/5.0101808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/02/2022] [Indexed: 06/17/2023]
Abstract
A new 320 GHz solid-state source interferometer is installed in the Heliotron J helical device to explore the physics of high-density plasmas (ne > 2-3 × 1019 m-3, typically) realized with advanced fueling techniques. This interferometry system is of the Michelson type and is based on the heterodyne principle, with two independent solid-state sources that can deliver an output power of up to 50 mW. A high time resolution measurement of <1 µs can be derived by tuning the frequency of one source in the frequency range of 312-324 GHz on the new system, which can realize the fluctuation measurement. We successfully measured the line-averaged electron density in high-density plasma experiments. The measured density agreed well with a microwave interferometer measurement using a different viewing chord, demonstrating that the new system can be used for routine diagnostics of electron density in Heliotron J.
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Affiliation(s)
- P Zhang
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - S Ohshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - H Zhao
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - C Deng
- University of California, Los Angeles, California 90095-1594, USA
| | - S Kobayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - S Kado
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - T Minami
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - R Matoike
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - A Miyashita
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - A Iwata
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Y Kondo
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - D Qiu
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - C Wang
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - M Luo
- Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - S Konoshima
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - S Inagaki
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - H Okada
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - T Mizuuchi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - K Nagasaki
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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14
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Lu M, Deng C, Sun Y, Wang D, Huang L, Liu P, Lin D, Cheng W, Hu G, Lin T, Yun B, Cui Y. Compact and broadband silicon mode-order converter using bricked subwavelength gratings. Opt Express 2022; 30:24655-24666. [PMID: 36237014 DOI: 10.1364/oe.462554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/13/2022] [Indexed: 06/16/2023]
Abstract
A compact and broadband silicon mode-order converter (MOC) scheme by employing reciprocal mode evolution between asymmetric input/output taper and bricked subwavelength gratings (BSWG) is proposed. In the proposed MOC, a quasi-TE0 mode is generated in the BSWG region, which can be regarded as an effective bridge between the two TE modes to be converted. Flexible mode conversion can be realized by only choosing appropriate structure parameters for specific mode transitions between input/output modes and the quasi-TE0 mode. By combing 3D finite difference time domain (FDTD) and particle swarm optimization (PSO) method, TE0-TE1 and TE0-TE2 MOCs are optimal designed, which can efficiently convert TE0 mode to TE1 and TE2 modes with lengths of 9.39 µm and 11.27 µm, respectively. Results show that the insertion losses of <1 dB and crosstalk of <-15 dB are achieved for both TE0-TE1 and TE0-TE2 MOCs, the corresponding working bandwidth are 128 nm (1511∼1639 nm) and 126 nm (1527∼1653 nm), respectively. Additionally, the MOCs can be fabricated with only single etch step with minimum feature size of 145 nm.
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15
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Huang L, Zhu X, Hu G, Deng C, Sun Y, Wang D, Lu M, Yun B, Zhang R, Zhang Y, Cui Y. Electrical Switching of the Off-Resonance Room-Temperature Valley Polarization in Monolayer MoS 2 by a Double-Resonance Chiral Microstructure. ACS Appl Mater Interfaces 2022; 14:22381-22388. [PMID: 35511437 DOI: 10.1021/acsami.2c03688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enhancing and expanding the manipulated range of room-temperature valley polarization at off-resonance wavelength is extremely crucial to developing various functional valleytronic devices. Although these have been realized through the double-resonance strategy or twist-angle engineering, the demand for electrical control over the concepts remains elusive. Here, we fabricate a gate-tunable double-resonance chiral microstructure using a molybdenum disulfides (MoS2) monolayer. On the basis of the varied interface charge density, we demonstrate the huge photoluminescence (PL) tuning ability of this configuration. Furthermore, benefiting predominately from the screening of long-range e-h exchange interactions and the chiral Purcell effect, the electrical switching of the room-temperature valley polarization at off-resonance wavelength is also realized. Our work enriches the functions of TMDs-based optoelectronic devices and may create important applications in future valley-polarized encode and information processing devices.
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Affiliation(s)
- Lei Huang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiaofan Zhu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Guohua Hu
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chunyu Deng
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yu Sun
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Dongyu Wang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Mengjia Lu
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Binfeng Yun
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ruohu Zhang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yan Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yiping Cui
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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Xia K, Wang F, Lai X, Luo P, Chen H, Ma Y, Huang W, Ou W, Li Y, Feng X, Lei Z, Tu X, Ke Q, Mao F, Deng C, Xiang A. Gene Editing/Gene Therapies: AAV-MEDIATED GENE THERAPY PRODUCES FERTILE OFFSPRING IN THE LHCGR-DEFICIENT MOUSE MODEL OF LEYDIG CELL FAILURE. Cytotherapy 2022. [DOI: 10.1016/s1465-3249(22)00156-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Hakala S, Vakkari V, Bianchi F, Dada L, Deng C, Dällenbach KR, Fu Y, Jiang J, Kangasluoma J, Kujansuu J, Liu Y, Petäjä T, Wang L, Yan C, Kulmala M, Paasonen P. Observed coupling between air mass history, secondary growth of nucleation mode particles and aerosol pollution levels in Beijing. Environ Sci Atmos 2022; 2:146-164. [PMID: 35419523 PMCID: PMC8929417 DOI: 10.1039/d1ea00089f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Atmospheric aerosols have significant effects on the climate and on human health. New particle formation (NPF) is globally an important source of aerosols but its relevance especially towards aerosol mass loadings in highly polluted regions is still controversial. In addition, uncertainties remain regarding the processes leading to severe pollution episodes, concerning e.g. the role of atmospheric transport. In this study, we utilize air mass history analysis in combination with different fields related to the intensity of anthropogenic emissions in order to calculate air mass exposure to anthropogenic emissions (AME) prior to their arrival at Beijing, China. The AME is used as a semi-quantitative metric for describing the effect of air mass history on the potential for aerosol formation. We show that NPF events occur in clean air masses, described by low AME. However, increasing AME seems to be required for substantial growth of nucleation mode (diameter < 30 nm) particles, originating either from NPF or direct emissions, into larger mass-relevant sizes. This finding assists in establishing and understanding the connection between small nucleation mode particles, secondary aerosol formation and the development of pollution episodes. We further use the AME, in combination with basic meteorological variables, for developing a simple and easy-to-apply regression model to predict aerosol volume and mass concentrations. Since the model directly only accounts for changes in meteorological conditions, it can also be used to estimate the influence of emission changes on pollution levels. We apply the developed model to briefly investigate the effects of the COVID-19 lockdown on PM2.5 concentrations in Beijing. While no clear influence directly attributable to the lockdown measures is found, the results are in line with other studies utilizing more widely applied approaches.
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Affiliation(s)
- S Hakala
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
| | - V Vakkari
- Finnish Meteorological Institute Erik Palmenin Aukio 1 Helsinki Finland
- Atmospheric Chemistry Research Group, Chemical Resource Beneficiation, North-West University Potchefstroom South Africa
| | - F Bianchi
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
| | - L Dada
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
- Extreme Environments Research Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL) Valais Sion 1951 Switzerland
- Laboratory of Atmospheric Chemistry, Paul Scherrer Institute 5232 Villigen Switzerland
| | - C Deng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing China
| | - K R Dällenbach
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
- Laboratory of Atmospheric Chemistry, Paul Scherrer Institute 5232 Villigen Switzerland
| | - Y Fu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing China
| | - J Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing China
| | - J Kangasluoma
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
| | - J Kujansuu
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
| | - Y Liu
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
| | - T Petäjä
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, Nanjing University Nanjing China
| | - L Wang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry (LAPC), Institute of Atmospheric Physics, Chinese Academy of Sciences Beijing 100029 China
| | - C Yan
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
| | - M Kulmala
- Aerosol and Haze Laboratory, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology Beijing China
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, Nanjing University Nanjing China
| | - P Paasonen
- Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki Helsinki Finland
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18
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Sun Y, Wang D, Deng C, Lu M, Huang L, Hu G, Yun B, Cui Y. Photonic generation of broadband linearly chirped microwave waveform based on a low-loss silicon on-chip spectral shaper. Opt Lett 2022; 47:1077-1080. [PMID: 35230294 DOI: 10.1364/ol.448246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A silicon on-chip spectral shaper based on a Sagnac loop incorporating a chirped multi-mode waveguide Bragg grating (WBG) for linearly chirped microwave waveform generation is fabricated and demonstrated. The transmission spectrum of the spectral shaper displays low insertion loss characteristic due to the application of edge coupling taper and multi-mode waveguide based grating. An up-chirped microwave waveform with bandwidth as large as 44 GHz is generated by mapping the spectrum profile of the spectral shaper to the temporal domain through a dispersion fiber. The instantaneous frequency of the generated signal shows good linearity benefiting from the weak modulation strength in the multi-mode WBG. The low insertion loss performance as well as the low dispersion value required in our design presents feasibility in further integration with on-chip dispersion.
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19
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Ma Y, Qiu F, Deng C, Li J, Huang Y, Wu Z, Zhou Y, Zhang Y, Xiong Y, Yao Y, Zhong Y, Qu J, Su J. Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19. Genome Med 2022; 14:16. [PMID: 35172892 PMCID: PMC8851814 DOI: 10.1186/s13073-022-01021-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/06/2022] [Indexed: 02/08/2023] Open
Abstract
Background Understanding the host genetic architecture and viral immunity contributes to the development of effective vaccines and therapeutics for controlling the COVID-19 pandemic. Alterations of immune responses in peripheral blood mononuclear cells play a crucial role in the detrimental progression of COVID-19. However, the effects of host genetic factors on immune responses for severe COVID-19 remain largely unknown. Methods We constructed a computational framework to characterize the host genetics that influence immune cell subpopulations for severe COVID-19 by integrating GWAS summary statistics (N = 969,689 samples) with four independent scRNA-seq datasets containing healthy controls and patients with mild, moderate, and severe symptom (N = 606,534 cells). We collected 10 predefined gene sets including inflammatory and cytokine genes to calculate cell state score for evaluating the immunological features of individual immune cells. Results We found that 34 risk genes were significantly associated with severe COVID-19, and the number of highly expressed genes increased with the severity of COVID-19. Three cell subtypes that are CD16+monocytes, megakaryocytes, and memory CD8+T cells were significantly enriched by COVID-19-related genetic association signals. Notably, three causal risk genes of CCR1, CXCR6, and ABO were highly expressed in these three cell types, respectively. CCR1+CD16+monocytes and ABO+ megakaryocytes with significantly up-regulated genes, including S100A12, S100A8, S100A9, and IFITM1, confer higher risk to the dysregulated immune response among severe patients. CXCR6+ memory CD8+ T cells exhibit a notable polyfunctionality including elevation of proliferation, migration, and chemotaxis. Moreover, we observed an increase in cell-cell interactions of both CCR1+ CD16+monocytes and CXCR6+ memory CD8+T cells in severe patients compared to normal controls among both PBMCs and lung tissues. The enhanced interactions of CXCR6+ memory CD8+T cells with epithelial cells facilitate the recruitment of this specific population of T cells to airways, promoting CD8+T cell-mediated immunity against COVID-19 infection. Conclusions We uncover a major genetics-modulated immunological shift between mild and severe infection, including an elevated expression of genetics-risk genes, increase in inflammatory cytokines, and of functional immune cell subsets aggravating disease severity, which provides novel insights into parsing the host genetic determinants that influence peripheral immune cells in severe COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01021-1.
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Affiliation(s)
- Yunlong Ma
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fei Qiu
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Chunyu Deng
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jingjing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Zhejiang, 310003, Hangzhou, China
| | - Yukuan Huang
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zeyi Wu
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yijun Zhou
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yaru Zhang
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yichun Xiong
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China
| | - Yinghao Yao
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China
| | - Yigang Zhong
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jia Qu
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, China. .,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
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Chen S, Wang Y, Wang Z, Zhang X, Deng C, Ma B, Yang J, Lu Q, Zhao Y. Sleep Duration and Frailty Risk among Older Adults: Evidence from a Retrospective, Population-Based Cohort Study. J Nutr Health Aging 2022; 26:383-390. [PMID: 35450995 DOI: 10.1007/s12603-022-1766-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVES Frailty and sleep duration complaints are both prevalent and often coexist among older adults. The purpose of this study was to examine the prospective association between sleep duration and frailty risk in a nationally representative cohort study. DESIGN Prospective cohort study, ten-year follow-up. SETTING Community-based setting in 23 provinces of China. PARTICIPANTS A total of 7623 older adults age 65 and over without frailty at baseline were included in the analysis. MEASUREMENTS The participants were divided into three groups according to self-reported sleep duration: short (≤6 hours per day), middle (>6 but <10 hours per day) and long (≥10 hours per day). Frailty was measured according to the accumulation of health deficits by the construction of a frailty index of 38 items with 0.25 as the cutoff. A Cox proportional hazard model, a competing risk model and a generalized estimating equation (GEE) model with multiple adjustments were performed to evaluate the association between sleep duration and frailty risk. RESULTS During a median follow-up period of 4.4 years (IQR 2.9-9.0), 2531 (33.2%) individuals developed frailty. Compared with participants with middle sleep duration, the risk of frailty was increased among participants with long sleep duration (HR 1.26, 95% CI 1.14-1.38) in the fully adjusted Cox proportional hazard model. However, short sleep duration was insignificantly associated with frailty risk. The competing risk model and the GEE model yielded similar results. CONCLUSION Long sleep duration is significantly associated with frailty incidence among older adults even after adjustment for confounding factors. This study provides reinforcing longitudinal evidence for the need to design sleep quality improvement interventions in health care programs to prevent frailty among older adults.
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Affiliation(s)
- S Chen
- Qi Lu, MD, School of Nursing, Tianjin Medical University, Tianjin, 300070, China. Tel:86-23542855. Email address: ; Yue Zhao, PhD, Professor, School of Nursing, Tianjin Medical University, Tianjin, 300070, China. Tel:86-23542855. Email address:
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21
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Xiang B, Deng C, Qiu F, Li J, Li S, Zhang H, Lin X, Huang Y, Zhou Y, Su J, Lu M, Ma Y. Single cell sequencing analysis identifies genetics-modulated ORMDL3 + cholangiocytes having higher metabolic effects on primary biliary cholangitis. J Nanobiotechnology 2021; 19:406. [PMID: 34872583 PMCID: PMC8647381 DOI: 10.1186/s12951-021-01154-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Primary biliary cholangitis (PBC) is a classical autoimmune disease, which is highly influenced by genetic determinants. Many genome-wide association studies (GWAS) have reported that numerous genetic loci were significantly associated with PBC susceptibility. However, the effects of genetic determinants on liver cells and its immune microenvironment for PBC remain unclear. RESULTS We constructed a powerful computational framework to integrate GWAS summary statistics with scRNA-seq data to uncover genetics-modulated liver cell subpopulations for PBC. Based on our multi-omics integrative analysis, 29 risk genes including ORMDL3, GSNK2B, and DDAH2 were significantly associated with PBC susceptibility. By combining GWAS summary statistics with scRNA-seq data, we found that cholangiocytes exhibited a notable enrichment by PBC-related genetic association signals (Permuted P < 0.05). The risk gene of ORMDL3 showed the highest expression proportion in cholangiocytes than other liver cells (22.38%). The ORMDL3+ cholangiocytes have prominently higher metabolism activity score than ORMDL3- cholangiocytes (P = 1.38 × 10-15). Compared with ORMDL3- cholangiocytes, there were 77 significantly differentially expressed genes among ORMDL3+ cholangiocytes (FDR < 0.05), and these significant genes were associated with autoimmune diseases-related functional terms or pathways. The ORMDL3+ cholangiocytes exhibited relatively high communications with macrophage and monocyte. Compared with ORMDL3- cholangiocytes, the VEGF signaling pathway is specific for ORMDL3+ cholangiocytes to interact with other cell populations. CONCLUSIONS To the best of our knowledge, this is the first study to integrate genetic information with single cell sequencing data for parsing genetics-influenced liver cells for PBC risk. We identified that ORMDL3+ cholangiocytes with higher metabolism activity play important immune-modulatory roles in the etiology of PBC.
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Affiliation(s)
- Bingyu Xiang
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Chunyu Deng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Fei Qiu
- Institute of Biomedical Big Data, School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jingjing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Shanshan Li
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Huifang Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Xiuli Lin
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yukuan Huang
- Institute of Biomedical Big Data, School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Yijun Zhou
- Institute of Biomedical Big Data, School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jianzhong Su
- Institute of Biomedical Big Data, School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China
| | - Mingqin Lu
- Department of Infectious Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Yunlong Ma
- Institute of Biomedical Big Data, School of Ophthalmology and Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
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22
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Jowsey T, Deng C, Weller J. General-purpose thematic analysis: a useful qualitative method for anaesthesia research. BJA Educ 2021; 21:472-478. [PMID: 34840819 DOI: 10.1016/j.bjae.2021.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- T Jowsey
- Centre for Medical and Health Sciences Education, School of Medicine, University of Auckland, Auckland, New Zealand
| | - C Deng
- Department of Anaesthesia, Auckland City Hospital, Auckland, New Zealand
| | - J Weller
- Centre for Medical and Health Sciences Education, School of Medicine, University of Auckland, Auckland, New Zealand.,Department of Anaesthesia, Auckland City Hospital, Auckland, New Zealand
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23
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Bi N, Hu X, Zhao K, Yang Y, Zhang L, E M, Cao J, Ge H, Zhu X, Zhao L, Di Y, Jiang W, Ran J, Zhang H, Zhang T, Shen W, Deng C, Hu C, Chen M, Wang L. P64.04 Hypo-Fractionated Versus Conventionally Fractionated Radiotherapy for Patients with LS-SCLC: An Open-Label, Randomized, Phase 3 Trial. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Janne P, Wang M, Mitchell P, Fang J, Nian W, Chiu C, Zhou J, Zhao Y, Su W, Camidge D, Yang T, Zhu V, Millward M, Fan Y, Huang W, Cheng Y, Jiang L, Brungs D, Bazhenova L, Lee C, Gao B, Qi S, Yu X, Deng C, Chen K, Ye X, Zheng L, Yang Z, Yang J. OA15.02 Phase 1 Studies of DZD9008, an Oral Selective EGFR/HER2 Inhibitor in Advanced NSCLC with EGFR Exon20 Insertion Mutations. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Chen S, Ye T, Fu F, Deng C, Hu H, Sun Y, Pan Y, Zhang Y, Xiang J, Zhang Y, Shen X, Wang S, Wang Z, Li Y, Chen H. P56.03 Prognostic Value of Tumor Spread Through Air Spaces in Patients With Lung Adenocarcinoma after Radical Surgery. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Ouyang DJ, Chen QT, Anwar M, Xie N, Ouyang QC, Fan PZ, Qian LY, Chen GN, Zhou EX, Guo L, Gu XW, Ding BN, Yang XH, Liu LP, Deng C, Xiao Z, Li J, Wang YQ, Zeng S, Wang S, Yi W. The Efficacy of Pyrotinib as a Third- or Higher-Line Treatment in HER2-Positive Metastatic Breast Cancer Patients Exposed to Lapatinib Compared to Lapatinib-Naive Patients: A Real-World Study. Front Pharmacol 2021; 12:682568. [PMID: 34512325 PMCID: PMC8428978 DOI: 10.3389/fphar.2021.682568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Pyrotinib is a novel irreversible pan-ErbB receptor tyrosine kinase inhibitor. Evidence of the efficacy of pyrotinib-based treatments for HER2-positive metastatic breast cancer (MBC) in patients exposed to lapatinib is limited. Methods: Ninety-four patients who received pyrotinib as a third- or higher-line treatment for HER2-positive MBC were included in this retrospective study. The primary and secondary endpoints were overall survival (OS) and progression‐free survival (PFS). Propensity score matching (PSM) and inverse probability of treatment weighting (IPTW) analysis were implemented to balance important patient characteristics between groups. Results: Thirty (31.9%) patients were pretreated with lapatinib and subsequently received pyrotinib as an anti-HER2 treatment, and 64 (68.1%) patients did not receive this treatment. The OS and PFS indicated a beneficial trend in lapatinib-naive group compared to lapatinib-treated group in either the original cohort (PFS: 9.02 vs 6.36 months, p = 0.05; OS: 20.73 vs 14.35 months, p = 0.08) or the PSM (PFS: 9.02 vs 6.08 months, p = 0.07; OS: 19.07 vs 18.00 months, p = 0.61) or IPTW (PFS: 9.90 vs 6.17 months, p = 0.05; OS: 19.53 vs 15.10 months, p = 0.08) cohorts. Subgroup analyses demonstrated lapatinib treatment-related differences in PFS in the premenopausal subgroup and the no prior trastuzumab treatment subgroup, but no significant differences were observed in OS. Conclusion: Pyrotinib-based therapy demonstrated promising effects in HER2-positive MBC patients in a real-world study, especially in lapatinib-naive patients, and also some activity in lapatinib-treated patients.
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Affiliation(s)
- D J Ouyang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Q T Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - M Anwar
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - N Xie
- Department of Internal Medicine of Breast, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Q C Ouyang
- Department of Internal Medicine of Breast, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - P Z Fan
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital, Changsha, China
| | - L Y Qian
- Department of Breast and Thyroid Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - G N Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - E X Zhou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - L Guo
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - X W Gu
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital, Changsha, China
| | - B N Ding
- Department of Breast and Thyroid Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - X H Yang
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - L P Liu
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - C Deng
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Z Xiao
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - J Li
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Y Q Wang
- Department of Traditional Chinese Medicine, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - S Zeng
- Department of Internal Medicine-Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
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27
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Deng C. O-044 Chinese Society of Reproductive Medicine 2018 annual report on ART. Hum Reprod 2021. [DOI: 10.1093/humrep/deab126.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract text
Objective
To analysis the Chinese ART data in 2018 to provide evidence for utilization of various ART.
Methods
The data of ART of 263 Reproductive Centers in the mainland of China in 2018 were collected by CSRM ART Data Reporting System. A cross-sectional survey of the use of ART technology was performed.
Results
In 2018, the CSRM data reporting system reported 105 610 AID/AIH cycles, 323 938 oocyte retrieval cycles, 147 129 fresh embryo transfer cycles, 254 012 frozen-thawed embryo transfer (FET) cycles, and 204 688 newborn . The patient's age was mainly concentrated in the group <35 years old, accounting for 63.75%. The pregnancy rate and live birth rate of retrieval cycles were 52.49% and 42.23% respectively. The pregnancy rate and live birth rate of FET cycles were 48.71% and 37.68% respectively. Among ART complications, the incidence of moderate to severe OHSS was 1.42%, 0.03% postoperative bleeding, 0.01% postoperative pelvic infection, and 0.04% the other complications. The incidence of birth defects of IVF was 0.87%.
Conclusions
This study uses "CSRM data reporting system" data to describe and analyze the current status of ART, basically consistent with the comparison in 2016 and 2017 that most cycles with good outcomes. However, no clear conclusions have been drawn on the changes of PGD/PGS cycle, all-freeze cycle and comprehensive analysis should be conducted by combining with laboratory data.
Trial registration number:
Study funding:
Funding source:
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Affiliation(s)
- C Deng
- Peking Union Medical College Hospital, IVF Center, Beijing, China
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Ke G, Chen X, Liao R, Xu L, Zhang L, Zhang H, Kuang S, Du Y, Hu J, Lian Z, Dou C, Zhang Q, Zhao X, Zhang F, Zhu S, Ma J, Li Z, Li S, He C, Chen X, Wen Y, Feng Z, Zheng M, Lin T, Li R, Li B, Dong W, Chen Y, Wang W, Ye Z, Deng C, Xiao H, Xiao J, Liang X, Shi W, Liu S. Receptor activator of NF-κB mediates podocyte injury in diabetic nephropathy. Kidney Int 2021; 100:377-390. [PMID: 34051263 DOI: 10.1016/j.kint.2021.04.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/10/2021] [Accepted: 04/22/2021] [Indexed: 01/19/2023]
Abstract
Receptor activator of NF-κB (RANK) expression is increased in podocytes of patients with diabetic nephropathy. However, the relevance of RANK to diabetic nephropathy pathobiology remains unclear. Here, to evaluate the role of podocyte RANK in the development of diabetic nephropathy, we generated a mouse model of podocyte-specific RANK depletion (RANK-/-Cre T), and a model of podocyte-specific RANK overexpression (RANK TG), and induced diabetes in these mice with streptozotocin. We found that podocyte RANK depletion alleviated albuminuria, mesangial matrix expansion, and basement membrane thickening, while RANK overexpression aggravated these indices in streptozotocin-treated mice. Moreover, streptozotocin-triggered oxidative stress was increased in RANK overexpression but decreased in the RANK depleted mice. Particularly, the expression of NADPH oxidase 4, and its obligate partner, P22phox, were enhanced in RANK overexpression, but reduced in RANK depleted mice. In parallel, the transcription factor p65 was increased in the podocyte nuclei of RANK overexpressing mice but decreased in the RANK depleted mice. The relevant findings were largely replicated with high glucose-treated podocytes in vitro. Mechanistically, p65 could bind to the promoter regions of NADPH oxidase 4 and P22phox, and increased their respective gene promoter activity in podocytes, dependent on the levels of RANK. Taken together, these findings suggested that high glucose induced RANK in podocytes and caused the increase of NADPH oxidase 4 and P22phox via p65, possibly together with the cytokines TNF- α, MAC-2 and IL-1 β, resulting in podocyte injury. Thus, we found that podocyte RANK was induced in the diabetic milieu and RANK mediated the development of diabetic nephropathy, likely by promoting glomerular oxidative stress and proinflammatory cytokine production.
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Affiliation(s)
- Guibao Ke
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xueqin Chen
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Ruyi Liao
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Lixia Xu
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Li Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Hong Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Sujuan Kuang
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yue Du
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Juan Hu
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhiwen Lian
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Caoshuai Dou
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Qianmei Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xingchen Zhao
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fengxia Zhang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Shuangshuang Zhu
- Department of Renal Pathology, King Medical Diagnostics Center, Guangzhou, Guangdong, China
| | - Jianchao Ma
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhuo Li
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Sijia Li
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chaosheng He
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xia Chen
- Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yingzhen Wen
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhonglin Feng
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Minghao Zheng
- School of Surgery (Orthopaedics), University of Western Australia, Crawley, Perth, Western Australia, Australia
| | - Ting Lin
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Ruizhao Li
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Bohou Li
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wei Dong
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Yuanhan Chen
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wenjian Wang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Zhiming Ye
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chunyu Deng
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Houqin Xiao
- Department of Nephrology, Binhaiwan Central Hospital, Dongguan, Guangdong, China
| | - Jie Xiao
- Department of Nephrology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xinling Liang
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Wei Shi
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.
| | - Shuangxin Liu
- Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China.
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Ohshima S, Zhang P, Kume H, Deng C, Miyashita A, Kobayashi S, Okada H, Minami T, Kado S, Adulsiriswad P, Qiu D, Luo M, Matoike R, Suzuki T, Konoshima S, Mizuuchi T, Nagasaki K. Development of a multi-channel 320 GHz interferometer for high density plasma measurement in Heliotron J. Rev Sci Instrum 2021; 92:053519. [PMID: 34243360 DOI: 10.1063/5.0043581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/12/2021] [Indexed: 06/13/2023]
Abstract
We report the development of a new interferometer with two stable, high-power, 320 GHz solid-state sources in Heliotron J. A heterodyne Michelson interferometer optical scheme is employed. Two solid-state oscillators are utilized as sources with a fixed frequency at 320 GHz and frequency tunable of 312-324 GHz. Quasi-optical techniques are used for beam transmission. The beam is elongated in the vertical direction with two off-axis parabolic mirrors and injected into the plasma as a sheet beam for the multi-channel measurement (>5 ch.). Passing through the plasma, the beam is reflected at a retroreflector-array installed at the vacuum chamber wall. The retroreflector-array is a bunch of retroreflector structures, which can suppress the beam refraction caused by plasma without much space inside a vacuum chamber unlike a single retroreflector and can facilitate the system design. The source, detectors, and the retroreflector-array are tested to evaluate their basic performance on a tabletop experiment.
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Affiliation(s)
- S Ohshima
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
| | - P Zhang
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - H Kume
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - C Deng
- University of California, Los Angeles, Los Angeles, California 90095-1594, USA
| | - A Miyashita
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - S Kobayashi
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
| | - H Okada
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - T Minami
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - S Kado
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - P Adulsiriswad
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - D Qiu
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - M Luo
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - R Matoike
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - T Suzuki
- Graduate School of Energy Science, Kyoto University, Kyoto 611-0011, Japan
| | - S Konoshima
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
| | - T Mizuuchi
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
| | - K Nagasaki
- Institute of Advanced Energy, Kyoto University, Kyoto 611-0011, Japan
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Deng C, Lu M, Sun Y, Huang L, Wang D, Hu G, Zhang R, Yun B, Cui Y. Broadband and compact polarization beam splitter in LNOI hetero-anisotropic metamaterials. Opt Express 2021; 29:11627-11634. [PMID: 33984939 DOI: 10.1364/oe.421262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
In this paper, theoretical modeling and numerical simulations of a high-performance polarization beam splitter (PBS) based on hetero-anisotropic metamaterials are proposed on the lithium-niobate-on-insulator (LNOI) platform. The hetero-anisotropic metamaterials constructed by sub-wavelength gratings (SWGs) can be regarded as effective anisotropy medium, which exhibits strong birefringence without breaking the geometrical symmetry, contributing to the formation of PBS. Rather than the principle of PBS based on beat-length difference of transverse electric (TE) polarization and transverse magnetic (TM) polarization, the device can realize polarization beam splitting in single beat length, and the footprint of the proposed PBS can be reduced to 8 µm × 160 µm (with S-bend). The simulation results show that the bandwidth is 185 nm (1450∼1634 nm) for TE polarization while the bandwidth is 85 nm (1490∼1575 nm) for TM polarization when the polarization extinction ratio is >20 dB. Furthermore, the insertion loss is less than 1 dB in the range of 1450 to 1650 nm, for both TE and TM polarization. Additionally, the proposed device proves strong robustness of the fabrication tolerance.
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31
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Sun S, Xu L, Zhang X, Pang L, Long Z, Deng C, Zhu J, Zhou S, Wan L, Pang B, Xiao Y. Systematic Assessment of Transcriptomic Biomarkers for Immune Checkpoint Blockade Response in Cancer Immunotherapy. Cancers (Basel) 2021; 13:cancers13071639. [PMID: 33915876 PMCID: PMC8037221 DOI: 10.3390/cancers13071639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/13/2021] [Accepted: 03/26/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The aim of our study was to evaluate the predictive performance of transcriptomic biomarkers to immune response. The study collected 22 transcriptomic biomarkers and constructed multiple benchmark datasets to evaluate their predictive performance of immune checkpoint blockade (ICB) response in pre-treatment patients with distinct ICB agents in diverse cancers. We found “Immune-checkpoint molecule” biomarkers PD-L1, PD-L2, CTLA-4 and IMPRES and the “Effector molecule” biomarker CYT showed significant associations with ICB response and clinical outcomes. These immune-checkpoint biomarkers and another immune effector IFN-gamma presented predictive ability in melanoma, urothelial cancer and clear cell renal-cell cancer. Interestingly, for anti-PD-1 therapy and anti-CTLA-4 therapy, the top-performing response biomarkers were usually mutually exclusive even though in the same biomarker category and most of biomarkers with outstanding predictive power were observed in patients with combined anti-PD-1 and anti-CTLA-4 therapy. Abstract Background: Immune checkpoint blockade (ICB) therapy has yielded successful clinical responses in treatment of a minority of patients in certain cancer types. Substantial efforts were made to establish biomarkers for predicting responsiveness to ICB. However, the systematic assessment of these ICB response biomarkers remains insufficient. Methods: We collected 22 transcriptome-based biomarkers for ICB response and constructed multiple benchmark datasets to evaluate the associations with clinical response, predictive performance, and clinical efficacy of them in pre-treatment patients with distinct ICB agents in diverse cancers. Results: Overall, “Immune-checkpoint molecule” biomarkers PD-L1, PD-L2, CTLA-4 and IMPRES and the “Effector molecule” biomarker CYT showed significant associations with ICB response and clinical outcomes. These immune-checkpoint biomarkers and another immune effector IFN-gamma presented predictive ability in melanoma, urothelial cancer (UC) and clear cell renal-cell cancer (ccRCC). In non-small cell lung cancer (NSCLC), only PD-L2 and CTLA-4 showed preferable correlation with clinical response. Under different ICB therapies, the top-performing biomarkers were usually mutually exclusive in patients with anti-PD-1 and anti-CTLA-4 therapy, and most of biomarkers presented outstanding predictive power in patients with combined anti-PD-1 and anti-CTLA-4 therapy. Conclusions: Our results show these biomarkers had different performance in predicting ICB response across distinct ICB agents in diverse cancers.
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Affiliation(s)
- Shangqin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Zhilin Long
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
| | - Chunyu Deng
- Wenzhou Research Institute, University of Chinese Academy of Science, Wenzhou 325001, China;
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Shuting Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Linyun Wan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
- Correspondence: (B.P.); (Y.X.)
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; (S.S.); (L.X.); (X.Z.); (L.P.); (J.Z.); (S.Z.); (L.W.)
- Correspondence: (B.P.); (Y.X.)
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Qi Z, Hu G, Liu B, Li Y, Deng C, Zheng P, Wang F, Zhao L, Cui Y. Plasmonic nanocavity for obtaining bound state in the continuum in silicon waveguides. Opt Express 2021; 29:9312-9323. [PMID: 33820362 DOI: 10.1364/oe.419815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Bound states in the continuum (BICs) have become a new trend in the area of metaoptics and nanophotonics. Strong interactions in electromagnetic fields are analogous to electron transitions in atoms, giving rise to BICs with vanishing radiative losses. However, it is still a great challenge to realize BICs in the lossy plasmonic systems. For this problem, we propose a supercavity-like plasmonic nanocavity consisting of an Au nanorod deposited inside an Au symmetric split ring, and explore the possibility of exciting quasi-BICs that own finite but high quality (Q) factors. In such hybrid configuration, the excited resonances can be easily engineered by modifying the rotation angle or the length of the Au nanorod. With the integration of such nanocavity in silicon (Si) waveguides, sharp transmission spectra could be achieved with fiber-chip in-parallel excitations and detections. Besides, the ultracompact geometry of this plasmonic nanocavity provides a route to boost enhanced electric fields, thus improving sensing performances significantly. Our study not only offers a novel platform for the realization of chip-scale quasi-BICs, but extends functionalities of photonic-plasmonic hybrid circuits.
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Huang L, Su H, Hu G, Wu S, Wang Y, Chen B, Wang Q, Deng C, Yun B, Zhang R, Cui Y. Highly efficient and controllable photoluminescence emission on a suspended MoS 2-based plasmonic grating. Nanotechnology 2020; 31:505201. [PMID: 32996469 DOI: 10.1088/1361-6528/abb1ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Being a new class of materials, transition metal dichalcogenides are paving the way for applications in atomically thin optoelectronics. However, the intrinsically weak light-matter interaction and the lack of manipulation ability has lead to poor light emission and tunable behavior. Here, we investigate the fluorescence characteristic of monolayer molybdenum disulfide on a metal narrow-slit grating, where a highly efficient, 471 times photoluminescence enhancement are realized, based on the hybrid surface plasmon polaritons resonances and the decreased influence of substrate. Moreover, the emitted intensity and polarization are controllable due to the polarization-dependent characteristic and anisotropy of grating. The manipulations of light-matter interactions in this special system provide a new insight into the fluorescent emission process and open a new avenue for high-performance low dimensional materials devices designs.
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Affiliation(s)
- Lei Huang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
| | - Huanhuan Su
- National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 People's Republic of China
| | - Guohua Hu
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
| | - Shan Wu
- Key Laboratory of Functional Materials and Devices for Informatics of Anhui Higher Education Institutes, Fuyang Normal University, Fuyang 236037 People's Republic of China
| | - Yongkang Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189 People's Republic of China
| | - Boyu Chen
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
| | - Qianjin Wang
- National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 People's Republic of China
| | - Chunyu Deng
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
| | - Binfeng Yun
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
| | - Ruohu Zhang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
| | - Yiping Cui
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing, Jiangsu 210096 People's Republic of China
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Charlesworth M, Deng C. Pilot randomised controlled trial reporting should be focused: a reply. Anaesthesia 2020; 75:1551. [DOI: 10.1111/anae.15199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 11/30/2022]
Affiliation(s)
| | - C. Deng
- Auckland City Hospital Auckland New Zealand
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35
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Fei Liang, Zhao J, Deng C. Construction and Functional Properties of Multifunctional Chitosan Hydrogel. Polym Sci Ser A 2020. [DOI: 10.1134/s0965545x20050120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ding Z, Deng C, Wang Z, Liu L, Ma X, Huang J, Wang X, Xuan M, Xie H. Comparison of contrast-enhanced ultrasound and contrast-enhanced computed tomography for the diagnosis of cervical lymph node metastasis in squamous cell carcinoma of the oral cavity. Int J Oral Maxillofac Surg 2020; 50:294-301. [PMID: 32739248 DOI: 10.1016/j.ijom.2020.07.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/29/2020] [Accepted: 07/09/2020] [Indexed: 02/08/2023]
Abstract
Early detection of cervical lymph node metastasis (CLNM) from squamous cell carcinoma (SCC) of the oral cavity remains challenging. This prospective study was performed to evaluate the ability of contrast-enhanced ultrasound (CEUS) to detect CLNM from oral cavity SCC. Additionally, its diagnostic value was compared with that of contrast-enhanced computed tomography (CECT). Forty-eight consecutive patients with SCC of the oral cavity were enrolled. All subjects were examined preoperatively with both CEUS and CECT. Subsequently, neck dissections were performed for these patients, and cervical lymph nodes separated from the surgical specimens were assessed histologically. The diagnostic performance of these two examinations was compared based on the results of histopathology. The sensitivity, specificity, accuracy, positive predictive value, negative predictive value, and Youden index for CEUS and CECT were 69.39% vs. 44.90%, 94.71% vs. 97.12%, 89.88%% vs. 87.16%, 75.56% vs. 78.57%, 92.92% vs. 88.21%, and 64.10% vs. 42.02%, respectively. A significant difference was observed in terms of sensitivity (P=0.024) and Youden index (rate difference 22.08%, 95% confidence interval 2.72-41.44%). Therefore, CEUS appears to be a promising diagnostic tool that is superior to CECT for detecting CLNM from SCC of the oral cavity, with a higher sensitivity.
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Affiliation(s)
- Z Ding
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - C Deng
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z Wang
- Department of Ultrasound, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - L Liu
- Department of Radiology, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - X Ma
- Department of Biotherapy, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - J Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - M Xuan
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - H Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Xiang L, Qi F, Jiang L, Tan J, Deng C, Wei Z, Jin S, Huang G. CRISPR-dCas9-mediated knockdown of prtR, an essential gene in Pseudomonas aeruginosa. Lett Appl Microbiol 2020; 71:386-393. [PMID: 32506497 DOI: 10.1111/lam.13337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/19/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022]
Abstract
Pseudomonas aeruginosa is a widely distributed non-fermentative Gram-negative opportunistic pathogen that is often responsible for nosocomial infections. Gene interference is a potentially valuable tool for investigating essential genes in P. aeruginosa. To establish a gene interference platform in P. aeruginosa, CRISPR system was used with an inactive Cas9 protein. The CRISPR-dCas9 system was cloned into pHERD20T, a shuttle vector with arabinose inducible promoter, and was further modified to target a regulatory gene prtR that is essential for the viability of P. aeruginosa. Cells expressing the prtR-targeting CRISPR interference (CRISPRi) showed growth defect in an arabinose dose-dependent manner. A high-throughput RNA sequencing analysis of bacterial cells with or without the CRISPRi-mediated prtR inhibition indicated that prtRis a global regulator affecting multiple biological processes. In conclusion, the CRISPR-dCas9-based gene knockdown system has been successfully implemented in P. aeruginosa and demonstrated to be an effective tool in the investigation of essential or difficult-to-inactivate genes in this species.
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Affiliation(s)
- L Xiang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - F Qi
- Department of Plastic and Burn Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - L Jiang
- Department of Plastic and Burn Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - J Tan
- Department of Plastic and Burn Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - C Deng
- Department of Plastic and Burn Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Z Wei
- Department of Plastic and Burn Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - S Jin
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - G Huang
- Department of Plastic and Burn Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Deng C, Ren BY, Huang XP, Tan JJ, Wu JJ, Wang W, Zhu C. Role of lymphocyte subsets and IL-17 in non-small cell lung cancer. J BIOL REG HOMEOS AG 2020; 34:319-326. [PMID: 32431141 DOI: 10.23812/19-449-16-l] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- C Deng
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
| | - B Y Ren
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
| | - X P Huang
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
| | - J J Tan
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
| | - J J Wu
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
| | - W Wang
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
| | - C Zhu
- Department of Oncology, Chongqing Three Gorges Central Hospital, Wanzhou District, Chongqing, China
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Yuan H, Yan M, Zhang G, Liu W, Deng C, Liao G, Xu L, Luo T, Yan H, Long Z, Shi A, Zhao T, Xiao Y, Li X. CancerSEA: a cancer single-cell state atlas. Nucleic Acids Res 2020; 47:D900-D908. [PMID: 30329142 PMCID: PMC6324047 DOI: 10.1093/nar/gky939] [Citation(s) in RCA: 364] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/08/2018] [Indexed: 12/12/2022] Open
Abstract
High functional heterogeneity of cancer cells poses a major challenge for cancer research. Single-cell sequencing technology provides an unprecedented opportunity to decipher diverse functional states of cancer cells at single-cell resolution, and cancer scRNA-seq datasets have been largely accumulated. This emphasizes the urgent need to build a dedicated resource to decode the functional states of cancer single cells. Here, we developed CancerSEA (http://biocc.hrbmu.edu.cn/CancerSEA/ or http://202.97.205.69/CancerSEA/), the first dedicated database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. CancerSEA portrays a cancer single-cell functional state atlas, involving 14 functional states (including stemness, invasion, metastasis, proliferation, EMT, angiogenesis, apoptosis, cell cycle, differentiation, DNA damage, DNA repair, hypoxia, inflammation and quiescence) of 41 900 cancer single cells from 25 cancer types. It allows querying which functional states are associated with the gene (or gene list) of interest in different cancers. CancerSEA also provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. In summary, CancerSEA provides a user-friendly interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of tens of thousands of cancer single cells and the corresponding PCGs/lncRNAs expression profiles.
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Affiliation(s)
- Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Guanxiong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Wei Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Zhilin Long
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Aiai Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tingting Zhao
- Department of Neurology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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Zhang X, Lan Y, Xu J, Quan F, Zhao E, Deng C, Luo T, Xu L, Liao G, Yan M, Ping Y, Li F, Shi A, Bai J, Zhao T, Li X, Xiao Y. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Res 2020; 47:D721-D728. [PMID: 30289549 PMCID: PMC6323899 DOI: 10.1093/nar/gky900] [Citation(s) in RCA: 667] [Impact Index Per Article: 166.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/25/2018] [Indexed: 12/13/2022] Open
Abstract
One of the most fundamental questions in biology is what types of cells form different tissues and organs in a functionally coordinated fashion. Larger-scale single-cell sequencing and biology experiment studies are now rapidly opening up new ways to track this question by revealing substantial cell markers for distinguishing different cell types in tissues. Here, we developed the CellMarker database (http://biocc.hrbmu.edu.cn/CellMarker/ or http://bio-bigdata.hrbmu.edu.cn/CellMarker/), aiming to provide a comprehensive and accurate resource of cell markers for various cell types in tissues of human and mouse. By manually curating over 100 000 published papers, 4124 entries including the cell marker information, tissue type, cell type, cancer information and source, were recorded. At last, 13 605 cell markers of 467 cell types in 158 human tissues/sub-tissues and 9148 cell makers of 389 cell types in 81 mouse tissues/sub-tissues were collected and deposited in CellMarker. CellMarker provides a user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Furthermore, a summarized marker prevalence in each cell type is graphically and intuitively presented through a vivid statistical graph. We believe that CellMarker is a comprehensive and valuable resource for cell researches in precisely identifying and characterizing cells, especially at the single-cell level.
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Affiliation(s)
- Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Fei Quan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Erjie Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Aiai Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Tingting Zhao
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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Ping Y, Xu C, Xu L, Liao G, Zhou Y, Deng C, Lan Y, Yu F, Shi J, Wang L, Xiao Y, Li X. Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids. Front Bioeng Biotechnol 2020; 8:12. [PMID: 32117908 PMCID: PMC7010597 DOI: 10.3389/fbioe.2020.00012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
Engineered organoids by sequential introduction of key mutations could help modeling the dynamic cancer progression. However, it remains difficult to determine gene paths which were sufficient to capture cancer behaviors and to broadly explain cancer mechanisms. Here, as a case study of colorectal cancer (CRC), functional and dynamic characterizations of five types of engineered organoids with different mutation combinations of five driver genes (APC, SMAD4, KRAS, TP53, and PIK3CA) showed that sequential introductions of all five driver mutations could induce enhanced activation of more hallmark signatures, tending to cancer. Comparative analysis of engineered organoids and corresponding CRC tissues revealed sequential introduction of key mutations could continually shorten the biological distance from engineered organoids to CRC tissues. Nevertheless, there still existed substantial biological gaps between the engineered organoid even with five key mutations and CRC samples. Thus, we proposed an integrative strategy to prioritize gene cascading paths for shrinking biological gaps between engineered organoids and CRC tissues. Our results not only recapitulated the well-known adenoma–carcinoma sequence model (e.g., AKST-organoid with driver mutations in APC, KRAS, SMAD4, and TP53), but also provided potential paths for delineating alternative pathogenesis underlying CRC populations (e.g., A-organoid with APC mutation). Our strategy also can be applied to both organoids with more mutations and other cancers, which can improve and innovate mechanism across cancer patients for drug design and cancer therapy.
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Affiliation(s)
- Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jian Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Harbin, China
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Deng C, Campbell D, Diprose W, Eom C, Wang K, Robertson N, Short TG, Brew S, Caldwell J, McGuinness B, Barber PA. A pilot randomised controlled trial of the management of systolic blood pressure during endovascular thrombectomy for acute ischaemic stroke. Anaesthesia 2019; 75:739-746. [DOI: 10.1111/anae.14940] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 01/03/2023]
Affiliation(s)
- C. Deng
- Department of Anaesthesia and Peri‐operative Medicine Auckland City Hospital Auckland New Zealand
| | - D. Campbell
- Department of Anaesthesia and Peri‐operative Medicine Auckland City Hospital Auckland New Zealand
| | - W. Diprose
- Department of Radiology Auckland City Hospital Auckland New Zealand
| | - C. Eom
- Department of Anaesthesia and Peri‐operative Medicine Auckland City Hospital Auckland New Zealand
| | - K. Wang
- Department of Anaesthesia and Peri‐operative Medicine Auckland City Hospital Auckland New Zealand
| | - N. Robertson
- Department of Anaesthesia and Peri‐operative Medicine Auckland City Hospital Auckland New Zealand
| | - T. G. Short
- Department of Anaesthesia and Peri‐operative Medicine Auckland City Hospital Auckland New Zealand
| | - S. Brew
- Department of Radiology Auckland City Hospital Auckland New Zealand
| | - J. Caldwell
- Department of Radiology Auckland City Hospital Auckland New Zealand
| | - B. McGuinness
- Department of Radiology Auckland City Hospital Auckland New Zealand
| | - P. A. Barber
- Department of Medicine University of Auckland Auckland New Zealand
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43
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Shen Q, Xu X, Deng C. Factor structure of the Pittsburgh sleep quality index in Chinese adolescents. Sleep Med 2019. [DOI: 10.1016/j.sleep.2019.11.966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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44
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Lin H, Ran W, Chen X, Wang B, Yang P, Li Y, Xiao Y, Wang X, Li G, Wang L, Han Y, Peng Y, Lang J, Liang Y, Tian G, Yuan D, Yang J, Deng C, Xing X. Whole-exome sequencing of tumour-only samples reveals the association between somatic alterations and clinical features in pancreatic cancer. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz431.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Deng C, Li QH, Yang LJ, Liang JJ, Mo YQ, Lin JZ, Zheng DH, Dai L. [Characteristics and clinical significance of body composition in gout patients]. Zhonghua Nei Ke Za Zhi 2019; 58:751-757. [PMID: 31594173 DOI: 10.3760/cma.j.issn.0578-1426.2019.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the characteristics of body composition (BC) in gout patients and its clinical significance. Methods: Consecutive gout patients were recruited between August 2017 and December 2018. Demographic information, clinical characteristics and comorbidities were collected. BC was assessed by bioelectric impedance analysis including body fat percentage (BF%), trunk and limb BF%, appendicular skeletal muscle index. Overfat was defined by BF% ≥25% for male and ≥35% for female. The association between BC and serum uric acid (sUA) was evaluated by multiple linear regression. Results: A total of 362 gout patients were recruited with median age 38 (30, 52) years, 96.1% (348/362) were male. Mean sUA was (551±133) μmol/L. The mean BF% was (25.8±6.4)% with 53.6%(194/362) patients overfat. Male gout patients with overfat showed more affected joints [4(2, 6) vs. 2(2, 5)], higher sUA [(576±126)μmol/L vs. (523±134) μmol/L], higher prevalence of dyslipidemia [70.1%(131/187) vs. 54.0%(87/161)], metabolic syndrome [60.8%(118/187) vs. 28.0%(47/161)], fatty liver [58.2%(113/187) vs. 35.1%(59/161)] and hypertension [44.4%(83/187) vs. 25.5%(41/161)] than male patients with normal fat (all P<0.05). Their BF%, trunk BF% and limb BF% were positively correlated with the numbers of affected joints, sUA, metabolic syndrome, fatty liver, and hypertension, respectively (r=0.154-0.435, all P<0.05). Multivariable linear regression suggested that BF% (β=4.29, P=0.020) and trunk BF% (β=9.11, P=0.007), but not limb BF%, were positively correlated with sUA. Conclusion: Overfat is very common in gout patients. The proportion of trunk fat in male patients is positively correlated with sUA. When assessing obesity in gout patients clinically, body composition analysis should be performed simultaneously.
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Affiliation(s)
- C Deng
- Department of Rheumatology and Immunology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
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Deng C, Xie R, Banfield C, Gupta P, Feeney C, Rojo R, Peterson M. 170 Forecasting Phase 3 Dose-Response for Abrocitinib, an Oral Janus Kinase 1 Selective Inhibitor, Using Investigator’s Global Assessment and Eczema Area and Severity Index. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Xiao L, Gong C, Ding Y, Ding G, Xu X, Deng C, Ze X, Malard P, Ben X. Probiotics maintain intestinal secretory immunoglobulin A levels in healthy formula-fed infants: a randomised, double-blind, placebo-controlled study. Benef Microbes 2019; 10:729-739. [PMID: 31965842 DOI: 10.3920/bm2019.0025] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Formula-fed infants are more susceptible to infectious diseases because they lack the maternal immune factors transferred from breast milk, while their own immune system is still immature. As timely probiotic administration was suggested to promote immune system development in formula-fed infants, this study aimed at assessing the safety and the effects of a probiotic supplement (Bifidobacterium infantis R0033, Bifidobacterium bifidum R0071, and Lactobacillus helveticus R0052) on mucosal immune competence and digestive function in formula-fed infants. Healthy infants (3.5-6 months old) were randomised to receive either probiotic- (n=66) or placebo-supplemented (n=66) formula once a day for four weeks. In the probiotics group, faecal secretory immunoglobulin A (SIgA) levels remained similar between visit 2 (baseline; V2) and visit 3 (end-of-treatment; V3), but decreased in the placebo group. Changes in SIgA levels following treatment (log10ΔV3-V2 [95%CI]) between the probiotic and placebo groups were statistically significant (23 ng/dl [-57;102] and -137 ng/dl [-212;-62], respectively (P=0.0044; ANCOVA)). While log10ΔV3-V2 [95%CI] for salivary SIgA levels increased in both groups, this trend was more pronounced in the probiotics than in the placebo group with an increase of 123 ng/dl [9;236] and 37 ng/dL [-72;147], respectively (P=0.2829; ANCOVA). The weekly average number of stools/day was significantly higher in the probiotics group compared to placebo during the last week of treatment for the per protocol population. There was no difference in microbiota composition or anthropometric parameters between groups. No serious adverse event was reported, and all adverse events were mild and unrelated to the product or study. Our results show that formula-fed infants receiving probiotics maintained higher faecal SIgA levels at the end of the four-week treatment period, suggesting a positive effect of probiotics on SIgA production. This study demonstrates the safety of this probiotic formulation in infants. Formula-fed infants may benefit from probiotics supplementation to sustain the development of mucosal immunity.
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Affiliation(s)
- L Xiao
- Department of Neonatology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China P.R
| | - C Gong
- Department of Pediatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 201204, China P.R
| | - Y Ding
- Department of Neonatology, First People's Hospital of Zhangjiagang, Soochow University School of Medicine, Jiangsu 215600, China P.R
| | - G Ding
- Department of Respiratory Medicine, Shanghai Children's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200040, China P.R
| | - X Xu
- Lallemand Health Solutions Inc., 6100 Avenue Royalmount, Montreal, QC H4P 2R2, Canada
| | - C Deng
- Biostime (Guangzhou) Health Products Ltd., 187 Lianguang Rd, East District, Economic and Technological Development District Guangzhou, China P.R
| | - X Ze
- Biostime (Guangzhou) Health Products Ltd., 187 Lianguang Rd, East District, Economic and Technological Development District Guangzhou, China P.R
| | - P Malard
- Biostime (Guangzhou) Health Products Ltd., 187 Lianguang Rd, East District, Economic and Technological Development District Guangzhou, China P.R
| | - X Ben
- Department of Neonatology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai 201204, China P.R
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Deng Y, Luo S, Deng C, Luo T, Yin W, Zhang H, Zhang Y, Zhang X, Lan Y, Ping Y, Xiao Y, Li X. Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability. Brief Bioinform 2019; 20:254-266. [PMID: 28968730 DOI: 10.1093/bib/bbx109] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 02/06/2023] Open
Abstract
Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial cancer pathways. Recently, there is considerable evidence showing that, mutual exclusivity reflects alternative functions in tumor initiation and progression, or suggests adverse effects of their concurrence. Given its importance, numerous computational approaches have been proposed to study mutual exclusivity using genomic profiles alone, or by integrating networks and phenotypes. Some of them have been routinely used to explore genetic associations, which lead to a deeper understanding of carcinogenic mechanisms and reveals unexpected tumor vulnerabilities. Here, we present an overview of mutual exclusivity from the perspective of cancer genome. We describe the common hypothesis underlying mutual exclusivity, summarize the strategies for the identification of significant mutually exclusive patterns, compare the performance of representative algorithms from simulated data sets and discuss their common confounders.
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Affiliation(s)
- Yulan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shangyi Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenkang Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
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Zhang Y, Liao G, Bai J, Zhang X, Xu L, Deng C, Yan M, Xie A, Luo T, Long Z, Xiao Y, Li X. Identifying Cancer Driver lncRNAs Bridged by Functional Effectors through Integrating Multi-omics Data in Human Cancers. Mol Ther Nucleic Acids 2019; 17:362-373. [PMID: 31302496 PMCID: PMC6626872 DOI: 10.1016/j.omtn.2019.05.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/23/2019] [Accepted: 05/15/2019] [Indexed: 01/18/2023]
Abstract
The accumulation of somatic driver mutations in the human genome enables cells to gradually acquire a growth advantage and contributes to tumor development. Great efforts on protein-coding cancer drivers have yielded fruitful discoveries and clinical applications. However, investigations on cancer drivers in non-coding regions, especially long non-coding RNAs (lncRNAs), are extremely scarce due to the limitation of functional understanding. Thus, to identify driver lncRNAs integrating multi-omics data in human cancers, we proposed a computational framework, DriverLncNet, which dissected the functional impact of somatic copy number alteration (CNA) of lncRNAs on regulatory networks and captured key functional effectors in dys-regulatory networks. Applying it to 5 cancer types from The Cancer Genome Atlas (TCGA), we portrayed the landscape of 117 driver lncRNAs and revealed their associated cancer hallmarks through their functional effectors. Moreover, lncRNA RP11-571M6.8 was detected to be highly associated with immunotherapeutic targets (PD-1, PD-L1, and CTLA-4) and regulatory T cell infiltration level and their markers (IL2RA and FCGR2B) in glioblastoma multiforme, highlighting its immunosuppressive function. Meanwhile, a high expression of RP11-1020A11.1 in bladder carcinoma was predictive of poor survival independent of clinical characteristics, and CTD-2256P15.2 in lung adenocarcinoma responded to the sensitivity of methyl ethyl ketone (MEK) inhibitors. In summary, this study provided a framework to decipher the mechanisms of tumorigenesis from driver lncRNA level, established a new landscape of driver lncRNAs in human cancers, and offered potential clinical implications for precision oncology.
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Affiliation(s)
- Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Zhilin Long
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China.
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Falchi L, Lue J, Montanari F, Marchi E, Amengual J, Sawas A, Deng C, Khan K, Kim H, Rada A, Malanga M, Francescone M, Soderquist C, Park D, Bhagat G, Sokol L, Shustov A, O'Connor O. TARGETING THE PERIPHERAL T-CELL LYMPHOMA (PTCL) EPIGENOME WITH ORAL 5-AZACYTIDINE AND ROMIDEPSIN: RESULTS AND CLINICAL-MOLECULAR CORRELATIONS FROM A PHASE 2 STUDY. Hematol Oncol 2019. [DOI: 10.1002/hon.135_2629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- L. Falchi
- Medicine; Columbia University Medical Center; New York United States
| | - J.K. Lue
- Medicine; Columbia University Medical Center; New York United States
| | - F. Montanari
- Medicine; Columbia University Medical Center; New York United States
| | - E. Marchi
- Medicine; Columbia University Medical Center; New York United States
| | - J.E. Amengual
- Medicine; Columbia University Medical Center; New York United States
| | - A. Sawas
- Medicine; Columbia University Medical Center; New York United States
| | - C. Deng
- Medicine; Columbia University Medical Center; New York United States
| | - K. Khan
- Medicine; Columbia University Medical Center; New York United States
| | - H.A. Kim
- Medicine; Columbia University Medical Center; New York United States
| | - A. Rada
- Medicine; Columbia University Medical Center; New York United States
| | - M. Malanga
- Medicine; Columbia University Medical Center; New York United States
| | - M.F. Francescone
- Medicine; Columbia University Medical Center; New York United States
| | - C.R. Soderquist
- Medicine; Columbia University Medical Center; New York United States
| | - D.C. Park
- Medicine; Columbia University Medical Center; New York United States
| | - G. Bhagat
- Medicine; Columbia University Medical Center; New York United States
| | - L. Sokol
- Malignant Hematology; Moffitt Cancer Center/University of South Florida; Tampa United States
| | - A.R. Shustov
- Medicine; University of Washington School of Medicine; Seattle United States
| | - O.A. O'Connor
- Medicine; Columbia University Medical Center; New York United States
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